[AMBER] how to convert the eigenvector projection to a free energy landscape plotting

From: ning via AMBER <amber.ambermd.org>
Date: Wed, 20 Jul 2022 11:24:22 +0800 (CST)

Hi, Amber community

      I tried to make a free energy landscape (FEL) about protein conformation changes during accelerated MD simulation. However, when trying the tutorial guidance (https://ambermd.org/tutorials/advanced/tutorial22/section3.php), some strange errors appeared. I don't know what happen about the version upgrade from amber14 to amber20. Anyway, I decided to use another way, such as dihedral angle method, to get the FEL plotting. Here is my cpptraj input commands:

Here is part1:
parm s.prmtop
trajin s_prod_amd1.nc
multidihedral BB phi psi resrange 1-58 out PhiPsi_1-58.dat
matrix dihcovar dihedrals BB[*] out dihcovar.dat name DIH
diagmatrix DIH vecs 6 out modes.dihcovar.dat name DIHMODES

Here is part2:
parm s.prmtop
trajin s_prod_amd1.nc
readdata PhiPsi_1-58.dat name BB
dataset mode torsion BB
readdata modes.dihcovar.dat name MyModes
projection evecs modes MyModes out dih.project.dat beg 1 end 6 dihedrals BB

When it finished, I got these files: PhiPsi_1-58.dat, modes.dihcovar.dat, dihcovar.dat, dih.project.dat. Now, how do I convert the dih.project.dat into a dataset for FEL plotting using cpptraj or other programs? If some errors appeared in my commands, please remind me, thanks!


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Received on Thu Aug 04 2022 - 13:34:59 PDT
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